Table 1 Differential gene regulation by (p) ppGpp in PstDC3000 and PssB728a
| Â | Â | Homolog genes inversely regulated | PstDC3000 (unique genes) | PssB728a (unique genes) | ||
|---|---|---|---|---|---|---|
Symbol | Functional classification (COGs) | Â | Up | Down | Up | Down |
| Â | Type III secretion system | 0 | 0 | 37 | 0 | 7 |
J | Translation, ribosomal structure and biogenesis | 4 | 0 | 2 | 0 | 3 |
A | RNA processing and modification | 0 | 0 | 0 | 0 | 0 |
K | Transcription | 13 | 9 | 8 | 1 | 4 |
L | Replication, recombination and repair | 4 | 8 | 15 | 0 | 8 |
D | Cell cycle control, cell division, chromosome partitioning | 2 | 1 | 1 | 0 | 1 |
V | Defense mechanisms | 1 | 0 | 11 | 0 | 6 |
T | Signal transduction mechanisms | 16 | 3 | 10 | 0 | 9 |
M | Cell wall/membrane/envelope biogenesis | 14 | 1 | 8 | 2 | 14 |
N | Cell motility | 5 | 0 | 1 | 0 | 3 |
U | Intracellular trafficking, secretion, and vesicular transport | 15 | 1 | 1 | 1 | 9 |
O | Posttranslational modification, protein turnover, chaperones | 4 | 0 | 5 | 0 | 2 |
C | Energy production and conversion | 15 | 0 | 7 | 1 | 3 |
G | Carbohydrate transport and metabolism | 9 | 0 | 9 | 1 | 8 |
E | Amino acid transport and metabolism | 20 | 1 | 15 | 1 | 9 |
F | Nucleotide transport and metabolism | 1 | 0 | 3 | 0 | 0 |
H | Coenzyme transport and metabolism | 6 | 0 | 2 | 0 | 1 |
I | Lipid transport and metabolism | 9 | 3 | 3 | 1 | 4 |
P | Inorganic ion transport and metabolism | 16 | 0 | 10 | 0 | 4 |
Q | Secondary metabolites biosynthesis, transport and catabolism | 3 | 0 | 16 | 2 | 19 |
S | Function unknown | 101 | 64 | 199 | 29 | 145 |
Total | Â | 258 | 91 | 362 | 39 | 259 |